Mammalian herbivores face daily challenges to efficient digestion and rely on their gut microbiomes to survive. The gut microbiome is exclusively responsible for the essential functions of dietary fiber fermentation and degradation of common toxic plant secondary compounds (PSCs). Therefore, changes in microbiome composition could have major negative impacts on digestive function. Parasites in the gut have repeatedly been shown to decrease host gut microbial diversity, but there has been little investigation of functional changes associated with these decreases. We investigated gut microbiome diversity and function of wild, herbivorous white-throated woodrats (Neotoma albigula) with and without parasites to understand associations between parasitism and the herbivorous gut microbiome. Woodrats were captured in Castle Valley, UT and screened for parasites using fecal flotation. For four days, animals were held in metabolic cages and fed their natural diet of Opuntia cactus, which is rich in dietary fiber and the microbially-degraded PSC oxalate. We inventoried the microbiome by sequencing 16S rDNA from feces after four days of cactus feeding. We quantified dry matter digestion and oxalate degradation to directly measure microbiome functions. Data were examined in context of parasite infection status to determine if there were differences between parasitized and parasite-free animals.
Results/Conclusions
Thirty-eight woodrats completed the cactus diet trial in May (15 animals) and October (23 animals), 2019. One coccidian (Eimeria sp.) and one nematode (Lamotheoxyuris ackerti) were identified in fecal floats, and overall parasite prevalence was higher in May (73.3%) than October (39.1%). Preliminary analyses based on animals with nematode infections and parasite-free animals show no significant differences in gut microbial Shannon diversity based on infection status in May 2019 animals (Wilcoxon rank sums test, p=0.203). However, woodrats with nematode infections had significantly different gut microbiome community structure than uninfected woodrats (Bray-Curtis dissimilarity, ANOSIM p=0.01). This difference was most strongly affected by lower relative abundance of several species of the dominant gut microbial family Muribaculaceae in parasitized animals. We found no significant differences in dry matter digestibility (Student’s t-test, p=0.246) based on nematode infection, and quantification of oxalate degradation is underway. Our preliminary results suggest that natural worm infections may decrease relative abundance of major microbial taxa in white-throated woodrats, though those taxonomic differences are not associated with differences in dry matter digestibility.